R: Plot a Summary of the Link Communities

plotLinkCommSummComm {linkcomm} | R Documentation

## Plot a Summary of the Link Communities

### Description

This function is called by `plot.linkcomm` to plot either connectedness or modularity of individual link communities.

### Usage

    plotLinkCommSummComm(x, clusterids = 1:x$numbers[3], summary = "conn",
            pie = FALSE, col = TRUE, pal = brewer.pal(11, "Spectral"),
            random = FALSE, verbose = TRUE, ...)

### Arguments

`x` | An object of class `linkcomm`.
`clusterids` | An integer vector of community IDs. Defaults to all communities.
`summary` | A character string specifying the community summary. Can be one of `"conn"`, `"mod"`, `"ld"` for connectedness, modularity, and link densities respectively. Defaults to `"conn"`.
`pie` | Logical, whether to plot a pie graph. If FALSE, a bar plot is plotted. Defaults to FALSE.
`col` | Logical, whether to colour each community differently. Defaults to TRUE.
`pal` | A character vector describing a colour palette to be used for colouring the link communities. Defaults to `brewer.pal(11, "Spectral")`.
`random` | Logical, whether to randomise the link colours. Defaults to FALSE.
`verbose` | Logical, whether to print the progress of the calculation to the screen. Defaults to TRUE.
`...` | Additional arguments to be passed to `plot`.

### Details

Here we describe the parameters for plotting link community summaries using:
`plot(x, type = "commsumm", type = "mod")`

### Value

A bar graph or pie chart.

### Author(s)

Alex T. Kalinka alex.t.kalinka@gmail.com

### References

Kalinka, A.T. and Tomancak, P. (2011). linkcomm: an R package for the generation, visualization, and analysis of link communities in networks of arbitrary size and type. Bioinformatics 27, 2011-2012.

### See Also

`plot.linkcomm`

### Examples

    ## Generate graph and extract link communities.
    g <- swiss[,3:4]
    lc <- getLinkCommunities(g)

    ## Plot the modularity of the link communities.
    plot(lc, type = "commsumm", summary = "mod")

[Package linkcomm version 1.0-14 Index]